Cobalt in PDB 9b2n: Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Monometal Center

All present enzymatic activity of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Monometal Center:
3.1.1.81;

The structure of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Monometal Center, PDB code: 9b2n was solved by M.Corbella, J.A.Bravo, A.O.Demkiv, A.R.Calixto, K.Sompiyachoke, C.Bergonzi, S.C.L.Kamerlin, M.Elias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.65 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	146.36, 109.08, 78.74, 90, 115.95, 90
R / Rfree (%)	21.3 / 22.3

The binding sites of Cobalt atom in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Monometal Center (pdb code 9b2n). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Monometal Center, PDB code: 9b2n:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Monometal Center


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Monometal Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:24.2 occ:0.75 OD2 A:ASP220 2.2 30.1 1.0 NE2 A:HIS198 2.2 23.4 1.0 NE2 A:HIS118 2.2 23.7 1.0 ND1 A:HIS120 2.2 25.0 1.0 O A:HOH412 2.2 34.8 1.0 O A:HOH413 2.4 32.6 1.0 CD2 A:HIS198 3.1 24.4 1.0 CE1 A:HIS120 3.1 28.3 1.0 CE1 A:HIS118 3.1 23.4 1.0 CE1 A:HIS198 3.2 27.8 1.0 CD2 A:HIS118 3.2 24.0 1.0 CG A:ASP220 3.2 30.6 1.0 CG A:HIS120 3.3 25.6 1.0 CB A:HIS120 3.6 24.9 1.0 CB A:ASP220 3.6 24.9 1.0 O A:HOH452 4.0 42.8 1.0 NE2 A:HIS120 4.2 25.9 1.0 ND1 A:HIS118 4.3 24.7 1.0 CG A:HIS198 4.3 23.5 1.0 ND1 A:HIS198 4.3 27.9 1.0 CG A:HIS118 4.3 23.5 1.0 CD2 A:HIS120 4.3 28.0 1.0 OH A:TYR223 4.3 30.6 1.0 OD1 A:ASP220 4.3 31.2 1.0 CD2 A:HIS123 4.4 29.2 1.0 NE2 A:HIS123 4.4 27.5 1.0 OD1 A:ASN122 4.6 31.9 1.0 CE1 A:TYR223 4.8 26.5 1.0

Cobalt binding site 2 out of 3 in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Monometal Center


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Monometal Center within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:22.8 occ:0.75 OD2 B:ASP220 2.1 33.3 1.0 NE2 B:HIS118 2.2 19.7 1.0 ND1 B:HIS120 2.2 27.4 1.0 O B:HOH499 2.2 29.1 1.0 O B:HOH497 2.2 31.5 1.0 NE2 B:HIS198 2.2 24.4 1.0 CD2 B:HIS118 3.1 22.2 1.0 CE1 B:HIS120 3.1 25.6 1.0 CG B:ASP220 3.2 27.5 1.0 CD2 B:HIS198 3.2 24.1 1.0 CE1 B:HIS118 3.2 22.7 1.0 CE1 B:HIS198 3.2 23.7 1.0 CG B:HIS120 3.2 26.1 1.0 CB B:HIS120 3.6 24.9 1.0 CB B:ASP220 3.6 25.6 1.0 O B:HOH522 3.7 46.8 1.0 NE2 B:HIS120 4.2 25.2 1.0 OD1 B:ASP220 4.3 24.2 1.0 CG B:HIS118 4.3 20.2 1.0 ND1 B:HIS118 4.3 23.9 1.0 ND1 B:HIS198 4.3 23.6 1.0 CD2 B:HIS120 4.3 24.9 1.0 CG B:HIS198 4.3 21.2 1.0 OH B:TYR223 4.4 29.7 1.0 CD2 B:HIS123 4.4 23.4 1.0 NE2 B:HIS123 4.5 25.0 1.0 OD1 B:ASN122 4.8 29.4 1.0 CE1 B:TYR223 4.9 23.0 1.0

Cobalt binding site 3 out of 3 in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Monometal Center


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Monometal Center within 5.0Å range: probe atom residue distance (Å) B Occ C:Co301 b:23.9 occ:0.78 O C:HOH450 2.1 16.6 0.6 OD2 C:ASP220 2.2 28.1 1.0 NE2 C:HIS118 2.2 17.6 1.0 NE2 C:HIS198 2.2 21.6 1.0 O C:HOH504 2.3 32.5 1.0 ND1 C:HIS120 2.3 23.8 1.0 CD2 C:HIS118 3.2 20.3 1.0 CD2 C:HIS198 3.2 22.2 1.0 CE1 C:HIS118 3.2 20.8 1.0 CE1 C:HIS120 3.2 23.3 1.0 CE1 C:HIS198 3.2 22.8 1.0 CG C:ASP220 3.2 26.2 1.0 CG C:HIS120 3.3 20.3 1.0 O C:HOH557 3.5 45.3 1.0 CB C:ASP220 3.6 23.7 1.0 CB C:HIS120 3.6 21.6 1.0 O C:HOH499 3.8 29.2 0.6 ND1 C:HIS118 4.3 20.6 1.0 ND1 C:HIS198 4.3 20.6 1.0 CG C:HIS118 4.3 20.6 1.0 CG C:HIS198 4.3 19.5 1.0 NE2 C:HIS123 4.3 26.4 1.0 NE2 C:HIS120 4.3 22.9 1.0 CD2 C:HIS123 4.4 26.8 1.0 OD1 C:ASP220 4.4 24.4 1.0 CD2 C:HIS120 4.4 21.7 1.0 OH C:TYR223 4.4 26.1 1.0 OD1 C:ASN122 4.6 34.9 1.0 CE1 C:TYR223 4.7 23.9 1.0

M.Corbella, J.Bravo, A.O.Demkiv, A.R.Calixto, K.Sompiyachoke, C.Bergonzi, A.R.Brownless, M.H.Elias, S.C.L.Kamerlin. Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases. Jacs Au V. 4 3519 2024.
ISSN: ESSN 2691-3704
PubMed: 39328773
DOI: 10.1021/JACSAU.4C00404